IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses

David Paez-Espino, I. Min A. Chen, Krishna Palaniappan, Anna Ratner, Ken Chu, Ernest Szeto, Manoj Pillay, Jinghua Huang, Victor M. Markowitz, Torben Nielsen, Marcel Huntemann, T. B.K. Reddy, Georgios A. Pavlopoulos, Matthew B. Sullivan, Barbara J. Campbell, Feng Chen, Katherine McMahon, Steve J. Hallam, Vincent Denef, Ricardo CavicchioliSean M. Caffrey, Wolfgang R. Streit, John Webster, Kim M. Handley, Ghasem H. Salekdeh, Nicolas Tsesmetzis, Joao C. Setubal, Phillip B. Pope, Wen Tso Liu, Adam R. Rivers, Natalia N. Ivanova, Nikos C. Kyrpides

Research output: Contribution to journalArticlepeer-review

68 Scopus citations

Abstract

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.

Original languageEnglish (US)
Pages (from-to)D457-D465
JournalNucleic acids research
Volume45
Issue numberD1
DOIs
StatePublished - Jan 1 2017

ASJC Scopus subject areas

  • Genetics

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